[BUG] Project Path Case Sensitivity Causes MCP Configuration Conflict in Claude Code on Windows

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

When using the Claude Code VS Code extension on Windows, I encountered an MCP configuration conflict caused by case sensitivity in project paths. The VS Code extension is case-sensitive to project paths, so the drive letter in the project path under the projects node in .claude.json must be changed to lowercase (e.g., c:/Users/...) for project-level MCP services to load properly. However, after manual modification, the Claude CLI / desktop app automatically overwrites the configuration on the next launch and regenerates the path with an uppercase drive letter (e.g., C:/Users/...). This not only breaks the VS Code extension again but also makes project-level MCP services unusable in other clients. As a result, project-level MCP services cannot work correctly across multiple clients at the same time.

What Should Happen?

The expected behavior is that the entire Claude ecosystem—encompassing the VS Code extension, CLI, and desktop app—should resolve Windows path case-sensitivity conflicts for project-level MCP configurations seamlessly. All clients should natively support Windows' case-insensitive file system when reading and writing project paths in the .claude.json file, eliminating the need for manual path edits. Specifically, when persisting project paths under the projects node, all tools should automatically standardize drive letters to a consistent, lowercase format (e.g., c:/Users/...) to align with the VS Code extension's requirements, and no client should automatically overwrite or revert this standardized path on subsequent launches. This will ensure that project-level MCP services load correctly and function reliably across all Claude clients simultaneously, without configuration mismatches or broken service access.

Error Messages/Logs

Steps to Reproduce

1. Set up the test environment on Windows 10/11: Install Visual Studio Code, the official Claude Code extension, and the Claude desktop app / CLI tool. Create a new test project folder at a standard Windows path (e.g., C:\Projects\MCP-Test).

2.Open the test project folder C:\Projects\MCP-Test in VS Code, and initialize project-level MCP services using the Claude Code extension. This automatically generates a .claude.json configuration file in the project root.

3.Open the auto-generated .claude.json file. The projects node will contain a project path with an uppercase drive letter (minimal example below):
json
{
"projects": {
"C:/Projects/MCP-Test": {
"mcpServers": {
"figma": {
"type": "http",
"url": "https://mcp.figma.com/mcp"
}
}
}
}
4.Attempt to load project-level MCP services in the Claude Code VS Code extension. The services fail to load due to the extension’s case-sensitive path validation.

5.Manually edit .claude.json to change the drive letter to lowercase to fix the VS Code issue (modified example below):
json
{
"projects": {
"c:/Projects/MCP-Test": {
"mcpServers": {
"figma": {
"type": "http",
"url": "https://mcp.figma.com/mcp"
},
}
}
}
6.Verify project-level MCP services work correctly in the VS Code extension after the manual edit.

7.Verify that project-level MCP services work correctly in the VS Code extension after the manual edit.
Launch the Claude desktop app or CLI tool and open the same test project, then wait for the client to synchronize the configuration.

8.Check .claude.json again: the client does NOT overwrite the lowercase path — it adds a new uppercase drive letter path entry (the configuration now has two duplicate paths in different cases):
json
{
"C:/Projects/MCP-Test": {
"mcpServers": {
},
"c:/Projects/MCP-Test": {
"mcpServers": {
"figma": {
"type": "http",
"url": "https://mcp.figma.com/mcp"
}
}
}
}

9.Confirm the final issue: The project-level MCP services only appear and work in the VS Code extension, and are not visible or functional in the Claude desktop app, CLI, or any other clients.

Claude Model

Sonnet (default)

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.96

Platform

Other

Operating System

Windows

Terminal/Shell

VS Code integrated terminal

Additional Information

_No response_